Documentation & Package Separation / Day 69

Today was spent equal parts writing comments & documentation and separating the packages used in the code. Documentation wise, I added two pages to the wiki on the jpf-prism repository: one to describe the command line interface (though not yet any problems with compiling it!), and one to describe how to specify a jpf-prism property. Tomorrow I hope to put up some examples on the Wiki as well. That brings me to my second point: separating packages. Recall that I was borrowing some classes from jpf-probabilistic, and that I had copied them into our repository. However, I didn't change the package names. So while this was not a big issue while also requiring jpf-probabilistic, I'm trying to free us of that requirement by excluding it. This means in some cases changing our classes so that the correct classes are being used. This was a fair bit of work, because apparently sometimes the behaviour didn't quite copy over to new class names, opting instead to try to find old (non-classpath-included) classes. But that was fairly straightforward to resolve, even if it was tedious.  I also cleaned up a few "TODO" comments in the code, by handling more corner cases or cleaning up output.